void gth_sa_show(GthSA *sa, GthInput *input, GtFile *outfp)
{
GthSAVisitor *sa_visitor;
gt_assert(sa && input);
gth_input_load_genomic_file(input, sa->gen_file_num, false);
gth_input_load_reference_file(input, sa->ref_file_num, false);
sa_visitor = gth_txt_sa_visitor_new(input,
GTH_DEFAULT_GS2OUT,
GTH_DEFAULT_DPMININTRONLENGTH,
6, /* XXX */
GTH_DEFAULT_SHOWINTRONMAXLEN,
GTH_DEFAULT_TRANSLATIONTABLE,
GTH_DEFAULT_SHOWSEQNUMS,
outfp);
gth_sa_visitor_visit_sa(sa_visitor, sa);
gth_sa_visitor_delete(sa_visitor);
}
void gth_chaining(GthChainCollection *chain_collection,
GtUword gen_file_num,
GtUword ref_file_num,
GthCallInfo *call_info,
GthInput *input,
GthStat *stat,
bool directmatches,
const GthPlugins *plugins)
{
GtUword i, numofsequences = 0;
GtArray *matches;
GthChainingInfo chaining_info;
void *matcher_arguments;
GtFile *outfp = call_info->out->outfp;
GthMatchProcessorInfo match_processor_info;
bool refseqisdna = gth_input_ref_file_is_dna(input, ref_file_num);
/* make sure matcher is defined */
gt_assert(plugins);
gt_assert(plugins->matcher_arguments_new);
gt_assert(plugins->matcher_arguments_delete);
gt_assert(plugins->matcher_runner);
/* init */
matches = gt_array_new(sizeof (GthMatch));
chaining_info_init(&chaining_info, directmatches, refseqisdna, call_info,
input, stat, gen_file_num, ref_file_num);
matcher_arguments =
plugins->matcher_arguments_new(true,
input,
call_info->simfilterparam.inverse || !refseqisdna
? gth_input_get_genomic_filename(input, gen_file_num)
: gth_input_get_reference_filename(input,
ref_file_num),
call_info->simfilterparam.inverse || !refseqisdna
? gth_input_get_reference_filename(input,
ref_file_num)
: gth_input_get_genomic_filename(input, gen_file_num),
directmatches,
refseqisdna,
call_info->progname,
gt_str_get(gth_input_proteinsmap(input)),
call_info->simfilterparam.exact,
call_info->simfilterparam.edist,
false,
0,
call_info->simfilterparam.minmatchlength,
call_info->simfilterparam.seedlength,
call_info->simfilterparam.exdrop,
call_info->simfilterparam.prminmatchlen,
call_info->simfilterparam.prseedlength,
call_info->simfilterparam.prhdist,
call_info->translationtable,
call_info->simfilterparam.online,
call_info->simfilterparam.noautoindex,
call_info->simfilterparam.maskpolyAtails,
false);
match_processor_info_init(&match_processor_info, matches, chain_collection,
directmatches, refseqisdna,
call_info->simfilterparam.online,
call_info->simfilterparam.inverse, stat,
&chaining_info,
call_info->simfilterparam.maxnumofmatches,
call_info->simfilterparam.rare,
call_info->fragweightfactor,
plugins->jump_table_new,
plugins->jump_table_new_reverse,
plugins->jump_table_delete);
if (call_info->simfilterparam.maxnumofmatches > 0 ||
gth_stat_get_matchnumdistri(stat)) {
/* alloc space of match number counter */
numofsequences = gth_input_num_of_ref_seqs(input, ref_file_num);
match_processor_info.matchnumcounter = gt_malloc(sizeof (GtUword) *
numofsequences);
/* init match number counter to 0 */
memset(match_processor_info.matchnumcounter, 0,
(size_t) numofsequences * sizeof (GtUword));
}
/* free input, which contains the virtual trees.
because vmatch loads the virtual trees into memory, too.
this prevents that the virtual trees are loaded twice. */
gth_input_delete_current(input);
/* call matcher */
if (call_info->out->showverbose)
call_info->out->showverbose("call vmatch to compute matches");
plugins->matcher_runner(matcher_arguments, call_info->out->showverbose,
call_info->out->showverboseVM, &match_processor_info);
/* free matcher stuff here, because otherwise the reference file is mapped
twice below */
plugins->matcher_arguments_delete(matcher_arguments);
/* free sequence collections (if they have been filled by the matcher) */
gth_seq_con_delete(match_processor_info.gen_seq_con);
gth_seq_con_delete(match_processor_info.ref_seq_con);
/* save match numbers of match number distribution, if necessary */
if (gth_stat_get_matchnumdistri(stat)) {
for (i = 0; i < numofsequences; i++) {
if (match_processor_info.matchnumcounter[i] > 0) {
gth_stat_add_to_matchnumdistri(stat,
match_processor_info.matchnumcounter[i]);
}
}
}
/* free match number counter */
gt_free(match_processor_info.matchnumcounter);
/* return if no match has been found */
if (!gt_array_size(matches)) {
if (call_info->out->comments)
gt_file_xprintf(outfp, "%c no match has been found\n", COMMENTCHAR);
gt_array_delete(matches);
return;
}
/* load genomic file back into memory */
gth_input_load_genomic_file(input, gen_file_num, true);
/* load reference file back into memory */
gth_input_load_reference_file(input, ref_file_num, true);
/* compute chains from matches */
calc_chains_from_matches(chain_collection, matches, &chaining_info,
gth_input_current_gen_seq_con(input),
gth_input_current_ref_seq_con(input),
call_info->simfilterparam.rare,
call_info->fragweightfactor,
plugins->jump_table_new,
plugins->jump_table_new_reverse,
plugins->jump_table_delete);
if (call_info->out->showverbose) {
call_info->out->showverbose("sort global chains according to reference "
"sequence coverage");
}
/* sort chains */
gth_chain_collection_sort(chain_collection);
/* free */
gt_array_delete(matches);
}
GtUword gth_sa_get_alignment_lines(const GthSA *sa,
unsigned char **first_line,
unsigned char **second_line,
unsigned char **third_line,
GtUword translationtable,
GthInput *input)
{
GtUword genomicstartcutoff, genomicendcutoff, genomictotalcutoff,
referencestartcutoff, referenceendcutoff, referencetotalcutoff;
GT_UNUSED bool reverse_subject_pos = false;
gt_assert(sa && first_line && second_line && third_line && input);
/* only for cosmetic reasons */
genomicstartcutoff = gth_sa_genomiccutoff_start(sa);
genomicendcutoff = gth_sa_genomiccutoff_end(sa);
genomictotalcutoff = genomicstartcutoff + genomicendcutoff;
referencestartcutoff = gth_sa_referencecutoff_start(sa);
referenceendcutoff = gth_sa_referencecutoff_end(sa);
referencetotalcutoff = referencestartcutoff + referenceendcutoff;
/* sequences */
unsigned char *gen_seq_orig, *ref_seq_orig;
GtUword cols = 0;
GthSeqCon *ref_seq_con;
/* make sure that the correct files are loaded */
gth_input_load_reference_file(input, gth_sa_ref_file_num(sa), false);
ref_seq_con = gth_input_current_ref_seq_con(input);
/* If the reverse complement of the genomic DNA is considered, this
opition is needed for correct output of the genomic sequence positions
by the function showalignmentgeneric() */
if (!gth_sa_gen_strand_forward(sa))
reverse_subject_pos = true;
/* get genomic sequence */
gen_seq_orig = (unsigned char*)
gth_input_original_genomic_sequence(input, gth_sa_gen_file_num(sa),
gth_sa_gen_strand_forward(sa))
+ gth_sa_gen_dp_start(sa);
/* get reference sequence */
if (gth_sa_ref_strand_forward(sa)) {
ref_seq_orig =
gth_seq_con_get_orig_seq(ref_seq_con, gth_sa_ref_seq_num(sa));
}
else {
ref_seq_orig =
gth_seq_con_get_orig_seq_rc(ref_seq_con, gth_sa_ref_seq_num(sa));
}
switch (gth_sa_alphatype(sa)) {
case DNA_ALPHA:
/* compute the two alignment lines */
cols = gthfillthetwoalignmentlines(first_line,
second_line,
gen_seq_orig +
genomicstartcutoff,
gth_sa_gen_dp_length(sa) -
genomictotalcutoff,
ref_seq_orig +
referencestartcutoff,
gth_sa_ref_total_length(sa) -
referencetotalcutoff,
gth_sa_get_editoperations(sa),
gth_sa_get_editoperations_length(sa),
0, /* linewidth not important here */
0, /* no short introns here */
NULL,/* therefore no shortintroninfo */
gth_sa_indelcount(sa));
*third_line = NULL;
break;
case PROTEIN_ALPHA:
/* compute the three alignment lines */
cols = gthfillthethreealignmentlines(first_line,
second_line,
third_line,
gth_sa_get_editoperations(sa),
gth_sa_get_editoperations_length(sa),
gth_sa_indelcount(sa),
gen_seq_orig +
genomicstartcutoff,
gth_sa_gen_dp_length(sa) -
genomictotalcutoff,
ref_seq_orig +
referencestartcutoff,
gth_sa_ref_total_length(sa) -
referencetotalcutoff,
translationtable);
break;
default: gt_assert(0);
}
return cols;
}
void gth_sa_echo_alignment(const GthSA *sa, GtUword showintronmaxlen,
GtUword translationtable,
bool wildcardimplosion, GthInput *input,
GtFile *outfp)
{
GtUword genomicstartcutoff, genomicendcutoff, genomictotalcutoff,
referencestartcutoff, referenceendcutoff, referencetotalcutoff;
bool reverse_subject_pos = false;
const unsigned char *gen_seq_orig, *ref_seq_orig;
GthSeqCon *ref_seq_con;
GtAlphabet *ref_alphabet;
gt_assert(sa && input);
/* only for cosmetic reasons */
genomicstartcutoff = gth_sa_genomiccutoff_start(sa);
genomicendcutoff = gth_sa_genomiccutoff_end(sa);
genomictotalcutoff = genomicstartcutoff + genomicendcutoff;
referencestartcutoff = gth_sa_referencecutoff_start(sa);
referenceendcutoff = gth_sa_referencecutoff_end(sa);
referencetotalcutoff = referencestartcutoff + referenceendcutoff;
/* make sure that the correct files are loaded */
gth_input_load_reference_file(input, gth_sa_ref_file_num(sa), false);
ref_seq_con = gth_input_current_ref_seq_con(input);
ref_alphabet = gth_input_current_ref_alphabet(input);
/* If the reverse complement of the genomic DNA is considered, this
opition is needed for correct output of the genomic sequence positions
by the function showalignmentgeneric() */
if (!gth_sa_gen_strand_forward(sa))
reverse_subject_pos = true;
/* get genomic sequence */
gen_seq_orig =
gth_input_original_genomic_sequence(input, sa->gen_file_num,
sa->gen_strand_forward)
+ gth_sa_gen_dp_start(sa);
/* get reference sequence */
if (gth_sa_ref_strand_forward(sa)) {
ref_seq_orig =
gth_seq_con_get_orig_seq(ref_seq_con, gth_sa_ref_seq_num(sa));
}
else {
ref_seq_orig =
gth_seq_con_get_orig_seq_rc(ref_seq_con, gth_sa_ref_seq_num(sa));
}
switch (gth_sa_alphatype(sa)) {
case DNA_ALPHA:
gthshowalignmentdna(outfp,ALIGNMENTLINEWIDTH,
gth_sa_get_editoperations(sa),
gth_sa_get_editoperations_length(sa),
gth_sa_indelcount(sa),
gen_seq_orig + genomicstartcutoff,
gth_sa_gen_dp_length(sa) - genomictotalcutoff,
ref_seq_orig + referencestartcutoff,
gth_sa_ref_total_length(sa) -
referencetotalcutoff,
gth_sa_gen_dp_start(sa) + genomicstartcutoff -
gth_sa_gen_offset(sa), referencestartcutoff,
gth_sa_gen_total_length(sa), showintronmaxlen,
ref_alphabet, reverse_subject_pos,
wildcardimplosion);
break;
case PROTEIN_ALPHA:
gthshowalignmentprotein(outfp, ALIGNMENTLINEWIDTH,
gth_sa_get_editoperations(sa),
gth_sa_get_editoperations_length(sa),
gth_sa_indelcount(sa),
gen_seq_orig + genomicstartcutoff,
gth_sa_gen_dp_length(sa) - genomictotalcutoff,
ref_seq_orig + referencestartcutoff,
gth_sa_ref_total_length(sa) -
referencetotalcutoff,
gth_sa_gen_dp_start(sa) + genomicstartcutoff -
gth_sa_gen_offset(sa), referencestartcutoff,
gth_sa_gen_total_length(sa), showintronmaxlen,
ref_alphabet, translationtable,
gth_input_score_matrix(input),
gth_input_score_matrix_alpha(input),
reverse_subject_pos, wildcardimplosion);
break;
default: gt_assert(0);
}
}
